Sovereign Effect
by Dragon Eternal
Summary: Post Game - Commander Shepard has experienced so much loss in her life. If she had a chance, one chance to go back and change the way things happened - would she take it? Mindoir, Torfan, Eden Prime... Vermire... could she change it?
1. Chapter 1

--

Commander Shepard

--

The sound of ice against the metal cup gave a delightful clink. Months gone after the Reaper known as Sovereign had fallen. Months flying by so fast. Allies gone, going to their respective people - the only one that remained was her Gunnery Chief. Liara to Ilos, Wrex to his kind, Garrus to the ... to the Specters. Tali went back to her flotilla after that gorgeous expanse of data plopped into her lap. And now... Commander Shepard was formally recognized to be removed from the general chain of command. Not replaced, not higher, not lower, in the Alliance. Just... beyond it - but then again, maybe that was for the best. No more crew than she required, and in time she wanted to get the entire ship replaced and humans gone. Every face reminded her a little too much of Alenko. The world flipped around whenever those migraines hit; accompanied with the weight of the events of the past and graves unburied on worlds beyond the horizon were just a bit much. Quite the hero.

"Commander Shepard?"

"Joker, what is it this time?"

"We've arrived at the Relay, Commander..."

"Good. Keep the bearing steady. Let me know of any incoming comm traffic from these colonies."

"Aye-aye Commander. Joker, out."

Commander Shepard placed the glass back on the table, watching the vid screen again, watching the movie shot on this very deck. Mindoir, Torfan, Eden Prime, now Vermire... Had to push past it. Simple thing to do. Brace up, get going. Though she hated going through those Mass Relays. The feedback flared her implants. It was getting close to that time she counted, watching Alenko laugh on the screen. She'd have to go under the knife and change out those implants before things got worse. Could end up paralyzed, but as is when those waves hit it she was helpless. The knock on the door slipped her out of her thoughts. "Who's there?" She slurred quietly. Overhead, she listened to the voice of Joker counting down.

Before she heard the response, the finality of the count reached its perishing point and the world exploded - rendering all in her vision to black.

--

Disclaimer - I dost not owneth that game diggity do-dad that is Mass Effect. The game is an amazing game, and here is simply my musing of a homage to a well written, well developed game.

--

"Doctor, she's waking up." That voice... Alenko? Was it something that simple? Was she really back? In that momentary lapse, the data of the Protheans slipped across her memories, their cryptic message and desperate call for help. All of it, the entirity of their hope and salvation dying almost as fast as she woke up. Then that feeling, that slow sick feeling of the universe bending around her snapped her into awakening. "Doctor, the Commander's back up again." It... wasn't Alenko... Couldn't be Alenko. "Had us worried there Commander... Really saved me back there."

She had to be dreaming. "Kaiden?" The whisper moved out. In his glory, the dark haired marine gave a bashful smile as he moved from leaning against the wall. It was then, that the migraine hit. A sledgehammer to the back of her head, with explosions of lights as the L2 implant fired off thousands of readings a second. She heard things slam against the wall and felt the room creak and groan in response to the sudden aftershock as she screamed to herself. The world broke and reconfigured itself, slowly working its reality back to its own devises, and the Commander found herself bound to the medical table. "Shepard! Come on Commander! Commander please, calm down! She's not steadying - get we need sedatives here now!" The voices shouted back to each other. It was like she could feel the ship. She could taste the metal as she writhed, feeling her mass effect fields wrapping and demanding, arguing with what crafted stability there was.

"D-doctor Chakwas, what's g-going on?" Her message slipped out as she felt her fingers squeeze and fit on the table. With a plunge of a needle, and a concerned shush, she began to feel a dreamless sleep move into her veins. She saw him... she knew it... he was there... right there...

Sleep... quiet.. Dreamless.. Faceless sleep. The hours succumbed to eternity as slowly she felt the permission to wake again. The polite gunmetal ceiling of the medical bay greeted her eyes and offered no reassurance. What was going on.. Was it all a dream? Her thick tongue tasted a coppery essence, and it made her try to move. Kaiden.. She saw him.. Didn't she? Never got the chance to tell him... Vermire.. "Shh.. Doc.. Is she going to be alright?" The voice spoke. She felt fingers against her head, caring and tender. Ash.. Maybe? A quiet groan moved in response as the Commander tried to open her eyes, only to find a thick gauze to block her view. "Oh shit!" The person jumped. "Wow that was creepy..."

"Please Williams... don't speak too loudly. The L2 implants may have fried a lot of her nerves. We aren't certain yet what senses are still in tact."

I'm fine. She tried to respond. Only to find that she couldn't speak for the moment. Her throat refused to move and those precious muscles couldn't work. She tried again, tried harder, till finally a croak moved out. "Commander Shepard... the Mass Effect field triggered your implants to flare... I would have to guess the shielding of the wires is wearing thin. We have to schedule you for a transplant.. You're ... Can you hear me, Commander?" The doctor... right? That's who was talking? Everything felt so heavy. "Pending repairs... we are currently derelict... I.. Have come to the conclusion that the shielding of your L2 implants have corroded and... the Mass Effect field of the Relay ..." The words drifted off in a growing sound of ringing and then of something wet coming from her ears.

From what she could tell, that caused another panic, and she was muffled and pushed around a little more before things subsided. Alenko...

--

Ashley Williams

--

"She's bleeding from her ears again..." The Gunnery Chief whispered. She tried not to cry at this moment. Tried so hard. The result were pressed lips anc clinched jaws. "Shit... I thought she was better... what's going on Doc?" She looked back at the doctor. The greying woman however, offered no real possitive answers. Only more theories. Not the Commander. Couldn't loose her like this. After a few more moments she had enough, and left the medical bay. The ship was a ghost of its former glory now. The famous ship almost imploded from the inside. As a result, everyone wore their suits inside and helmets on, in case of another catastrophe. It was enough to make her want to hit something. Unlucky for Joker, she was headed his way for answers.

The woman popped her knuckles as she walked up the stairs. Time and again, the a-grav gave out, fighting to stay stable. Why did everyone have to leave? If Tali were here the problems would be fixed by now. If Liona were here they might have answers about biotics. Hell if Wrex were here she'd have someone to hit. But no! They were all gone and now its burden saddled on her. Ngh... Even Garrus left. That was... that hurt. She pressed the pad and opened the door, watching the rest of the crew salute her accordingly. The LT was supposed to be asleep right now, but in general people didn't question her authority. Not after the stuff she went through.

"Joker, you better give me some good news."

"I think I may have some for you soon."

"Is that so? Does it include a ride out of here?"

"I think so.. Listen to this."

She continued walking up and finally reached to where she didn't need to raise her voice. "Normandy? This ..." the static broke the message. ... "... floatilla, we received your distress call and are..." Despite the white noise... that voice, it sounded familiar. Sounded very familiar.

"Now this is what I call good news."

"Yeah, you can add it to the list of medals the Commander already owes me."

"You get us out of here and I'll get you a bottle of non-alcoholic Scotch."

"Non-alcoholic?"

"That's what it says anyway."

"I knew there was a reason I liked you."

"Save it for shore leave. Send the Floatilla the clearest message we can that -"

"Yes yes yes, I know. I'm the pilot remember, please."

"I'm going to cap you one day."

"And that's why I don't leave this chair."

Easy Commander... help is coming.

--

Fin

A short introduction to the story. The story itself will change points of view around once a chapter. Eventually it will settle down to being the Commander alone if everything works out that way. As is, everything is quite up in the air.


	2. Chapter 2

–

Commander Shepard - Alpha Timeline

--

Sand slipped through her fingers as moments of clarity and with each sating the hourglass. How long had it been, since she could speak? Or stand, for that matter. Most of her pleasant boring time grated her nerves. As much as she was awake anyway. Hearing came and went as she heard the passive grace of a respirator being used. "Commander Shepard, can you hear me?" A voice - a lilting voice with a strange accent... what? Who was bothering her now? The groan in response seemed to be satisfactory before the person would speak again. "Respect to your ancestors, Commander Shepard." The respirator hiccuped between his words. "Your hearing may go soon once more, so I will be brief... I am Admiral nar Rayya of the Quarian Flotilla. Our mechanics are working on your ship and you are currently in tow towards Citadel Station. It has been..." Slowly then, the words faded, and the migraine slowly worked its way back through her system.

Though it was mild, removed, and abating almost as quickly as it had come. It took her a few more seconds of wriggling on the table before she fell back, resting with a pressed breath. And still, the easy calm of the respirator continued. It was patient, it was even. She could measure her own lungs to its span. Her eyes, her face covered in gauze, restrained and matted with fever break. She was there, she knew it. She could feel it. She had seen Kaiden and that was all that truly mattered now. If she could just figure out how... "Are you still with me, Commander Shepard?" The thick gauze cut the light away from her eyes. Kept it from touching. Her hearing was just barely able to make out the sound of a suit's arms crossing. Then there was a small, inconsistent buzzing. Something off the range she could barely make out. A small nod was all she could afford, tired of taxing her throat.

"Good. I have a lot to thank you for, Commander. You cannot die just yet."

– – – – – – –

Disclaimer: I don't own Mass Effect. I'm just writing tidbits to put my two cents of nonsense into existence. That last one was a bit of a stretch.

Now this is where things are going to get messed up a little. Alpha Chronicle is the progression of the game itself, where Commander Shepard has already defeated Sovereign and lost Kaiden. Beta Chronicle however, is the incident where the Commander has shifted back into time, shortly after the incident on Eden Prime.

– – – – – – –

Defying gravity was not an easy thing. Artificial or not, it still could be quite a taxing ordeal. The Commander knew this of course, which is why she took a bit of pride in insulting the strength of the ship's A-grav drive - at much dismay to Doctor Chakwas. "You can either count for me or get out." Sweat dropped from her chin and met a salty little pool. The Gunnery Chief shook her head and made her way over, sitting on one of the out stretched tables. Denying her condition, the Specter resumed doing pushups, her knuckled braced against the floor and breath plastering the sweaty resin to the ground. Clad in what she deemed regular clothing, the Commander was happy to be able to take care of matters herself once more. Even if it hurt.

"Oh come on, you call that a pushup?"

"Shut up Williams."

"If you want you can do them girly style, I won't tell anyone."

"I said shut up Williams!"

"Fine, fine. That was three by the way."

"WILLIAMS!"

The Specter hit the deck, with a grimace and a growl. She heard the Gunnery Chief's feet touch the deck once more. Antagonizing her, eh? That was the plan? Whatever... That hurt. "Commander? You alright there?" The voice took a sisterly tone again. Like a kid trying to play the big sister. It annoyed Shepard. Aside from the uncomfortable position she now find herself in, she did not need Ash trying to be a nursemaid. It took a moment for the Commander to brace back up, resting on a heel. Bandages still covered her eyes but of current, a simple measure to dampen the light. Chakwas insisted that the less pressure on the back of her skull the better - so goggles were out for now; and despite all the movies of old, sunglasses were not military issue currently. Not on this ship anyway. "Not gonna try and kick my butt now are you?"

"No. I'm not." Shepard sucked on her canine for a brief moment before elaborating. The weight of her red tresses were gone. Shaved, so the doctor could inspect better, she hated the cold feeling whenever she moved. Made her have goose-bumps all down her arms. Nah.. Just stew on this moment a bit more. Let Williams have a little more comfort, she thought to herself. The specter let out a slow breath, offering a hand to the Chief who helped her up. Now, the bomb. "You're just on duty to clean the dishes tonight Williams." She heard the sputtering response and could not help a grin, making her way out of the med bay, "All of them."

"That's just cold."

She didn't know what she looked like. The mirrors could not give an accurate description due to the fuzzy white cat she wore over her eyes. Though from the dancing language of the crew, she had a feeling it wasn't pretty. Her senses sharpened slightly, picking up motions of air across her skin, vibrations through the ship in her toes. Though it was the hearing that really disturbed her. Enough that she still bore bandages upon them. Making her way up the stairs, she gave a nod to a soldier making his way to the mess. Their Quarian guests should be about, though she hadn't heard any of their breathing apparatus as of late. The admiral seemed to have made it his personal duty to watch over her like a mother hen with guns. He lost that charge to Williams - who was now going to be up to her elbows in antibacterial soap. "Ten-hut! Commander on Deck!" She hated that.

She looked over to the soldier. The doors had just finished clearing and he had already snapped a crisp salute that she could cut paper on. Couldn't go anywhere in her ship without people walking on eggshells. "At ease. I don't have a gun on me yet." The soldier's weight shifted as he nervously lowered his arm and looked a bit sheepish. Others had let out a soft chuckle but the Commander was already pressing on. She looked about, clasping her hands behind her back. Blindfolded and ears stuffed she could navigate this ship. Made her feel a little more like the Specter everyone thought she was. "Presley, where are you?" She sounded out, standing still.

"Ah, right here ma'am. Are you alright Commander you're sweating..."

"Soldiers are made out of sweat and blood, nothin' new here. Now, how long before we begin entering Citadel Space?"

"We have an incoming Asaari ship that has been provided by the Council to taxi you the rest of the way."

"So we can't make it by ourselves?"

"We are still moving at less that thirty four percent speed; while the repairs our Quarian guests have made go a long way, they simply don't have all the parts."

"XO, we're going to have a talk later."

"Yes ma'am."

"What did I say about guests on my ship, XO?"

"Yes ma'am, I remember ma'am."

"Alright then."

She strode past, making her way up the small plank. Ngh. They really had to clean this place a little better next time. That and use a disinfectant that wasn't so strong. The barefooted Commander began to hear the sounds of the familiar respirator up towards the bow, along with the quieter, smoother one she began to recognize as Tali's own. "Hey Commander, I'm steering the ship with no hands." Haha Joker. She mentally kicked the man, or would have liked too had she the energy to sum up such an action. The words did get a rebuke from Tali, who gave a warm greeting. The Admiral however, gave his customary, simple greeting. "Oh come on, the Commander knows I'm just kidding her."

"Uhuh. Enough small talk. I understand we have an Asaari ship on the way?" The Commander shifted her weight, giving a note to where everyone was positioned. The only person that seemed to be trying to ignore her affliction period would be the Admiral. "Any VIP's?" It was a refreshing notion.

"An Asaari Specter is on board Commander - it appears to be her ship."

"That's pleasant. The face got a name?"

"Aww I have to put a name to her - that just spoils everything Commander."

"So you have just the first name."

"Niobe, Commander. She says the Council sent her because she was nearby. Which means..."

"Which means she could have been across in another Nebula about to gun something down when they called."

"But that's just me Commander."

"ETA?"

"ETA ten minutes."

"Fantastic."

"Yeah - big whoop. Another Specter on board."

Someone smacked him over the back of the head. Probably Tali. "Father." She hissed. Okay, probably not. The Commander was trying to keep her lips placid, listening to the respirators whirring around her. She heard the small slow buzzing still, but now it was a lot more active. Like it was all over the place. Maybe electronics? "Are you... feeling better Shepard?" Tali's curious tone jogged her thoughts from their path of focus, and her hearing disappeared again with a ringing that grew louder and louder. Bringing a hand to an ear she swayed under the press and found support against an alien hand.

The Admiral's quiet touch supporter her for a moment. It seemed to have caught Tali off guard, with an almost inquiring tilt to her frame. Slowly afterwards, the Specter's sight began to wane as well, fading darker to oblivion as her fingers took a grip upon the wrist that supported her. All that could be measured were her own breaths and her own heart. The fingers of the metallic glove prickled hairs as it seemed to indicate a direction. The Commander shifted her weight a bit. Was the Admiral trying to ensure she saved face or make sure she didn't fall? She began to smell scarlet rivulets press against the gauze, but felt them hold true. Every hair at attention told her of the moving shapes, at least that was still hers to interpret. Shapes moved, and felt someone press the air off of her, moving ahead before Admiral and Commander followed in suit. Tali? Possibly. Warmed shame flushed her cheeks. So much for getting better, she bristled. The Commander's breath pressed in awkward strides as she tensed the humility down and swallowed it, pressing her shoulders back and moving as a soldier once more.

She only hoped she was doing it as efficiently as she hoped.

The Commander recognized the path chosen, and the gusts of wind moving from opened doors or the jerked motions of salutes. Towards the conference room - she mused. The small slope was a gracious move, as the Admiral's hold left her arm, and smaller hands took place. These fingers quivered for a moment as they nervously moved towards a seat. She could tell from the body heat simply radiating off of these two that it was Tali that now led, and the Admiral watched. Without the gift to hear, she nervously shortened her steps to an almost hobbling fashion, then rested once reprieve was assured. As soon as it was guaranteed, her hands shot to her bandages and began pulling at them. Small hands held and tried to keep the Specter from success yet.

The motions continued for a few motions till the Commander began to feel a cold feeling creeping up upon her. A quick chill swallowed her, and the struggle to free herself died. Kaiden... Where were you now? The silence blanketed, deafened, and smothered her conscious as she leaned against a cold shoulder, finding herself in a dizzying spiral to sleep.

--

Commander Shepard - Beta Timeline

--

"Captain Anderson, she's waking up." A familiar voice began moving to her ears. Doctor Chakwas... did she pass out again? How long were these attacks going to be bothering her. A quiet grunt was all that returned to the voice from the Specter. As she began to lift her head from the pillow, the weight was completely different. Where were her bandages? The light trickled through and she squinted her eyes tight, frustrated and grunting a little more as she brought her hands to cover. Meeting then, with soft fingers, the red bangs she had shaved months ago. What...? What was going on? "Commander Shepard? Are you alright? Alenko, please turn down the lights." Alenko?

The Commander shot up then and looked around and regretted it almost instantly with the jolt of wavering senses. The mewled wince slipped from her as she curled little more. She was aware then, of the beat of her heart, noted on a monitor, and growing still more accustomed to the feeling of the needles and tubes tying her. "What... what happened?" She whispered. The heat slowly melted down from her form, and the notions wavered and settled down. What was going on? How long had... Alenko? How had...

"You .. Saved me from the Beacon, Commander." His voice - his voice... It had to be Alenko. Was she sleeping? Why was she so scared to open her eyes? Open your eyes you big dummy. The inner voice bashed a little against her cowardice. If she didn't see him, she didn't have to say goodbye again...

The sound of the Captain's voice broke the train of thought in twine. "Commander Shepard... Commander Shepard are you still with us?" The red head's eyes opened up. She swallowed the thick little dancing frog in her throat and surveyed the room. The Doctor, the Captain, and..

"Alenko."

He smiled bashfully. That muscled jug head of his pressed a little in worry as the biotic shifted his weight. "Glad to see you're awake Commander." The man said in response. The thoughts trailed into Shepard's mind - was it all just a dream, all that she'd gone through? All that pain, all that fighting? What was going on? The emotions nipped her eyes and caused her to close them to hold them back, batting them for a few times to reign in the sensations. "Thought we had lost you too." Too? The words swam in her memory - Jenkins... The memories left from the beacon, the planets visited, all the knowledge ran towards her, blazing its way through her mind. Only fade with quick recession.

"Commander?"

"Y-yeah.. Just glad we didn't lose another."

The others shifted their weight, the Doctor patiently going to the machines that kept the Commander tethered. They new her history. They wouldn't question - hopefully. "You've been unconscious for a while now, Commander. Due to irregular health readings, I'm going to have to submit a due medical opinion that you should reside on the Normandy until your condition has stabilized." Citadel... wait.. What? "In interest to your health, Commander. Though it wouldn't be the first time a soldier has ignored a doctor's advice." Chakwas held a tone of amusement, finishing her tapping on the various boards.

"I'll be fine." She lied. Pulling out the various restraints with a growing ire, the Commander tried to keep her voice calm. "Besides... we still have to nail Saren." The name struck a cord, and everyone else shifted, giving a light nod. The Commander though, gave a light other motion of discomfort. What was she forgetting? Something important, she knew. But as she settled back down to the floor with unsettled feet, she felt Kaiden's comforting touch, against her shoulder. Everything was going to be alright... Alenko was back. They'd get Saren for Eden Prime. And figure out what else was going on. She couldn't help but feel that tingling scream in the back of her head, telling her she was forgetting something. Something important. That could save thousands of lives.

But for the life of her, she didn't care... not right now.

The Captain cleared his voice. "Doctor Chakwas, if you and LT Alenko wait outside, I'd like to clear a few things up with the Commander before we dock." They nodded, giving their words of affirmation before heading out. The Captain waited, watching them leave quietly before nodding and crossing his arms. "Are you alright soldier?" He spoke. It took a tone of concern she hadn't heard in a while. Though maybe her head was just swimming from before. She nodded, smiling a bit. "Good. Saren is out there... I .. Don't know if I'm happy with the way things are going now... but you .. Your career needs this. The Specters would be at an incredible advantage, and we just have to make sure that things that have happened don't jeopardize your credibility."

"I'll be alright Captain, just let the politicians do their thing and I'll do my job."

To that, the veteran smiled. "You are an amazing woman Commander."

"Captain?"

"See you topside. I'll be at the Ambassador's office. Williams is aboard, pending questioning with yourself and Alenko."

A moment of confusion still stayed on her features as the Captain left. Huh? What... what was that? For a moment there she could've sworn he was coming onto her. Ngh - she just needed a good bowl of synthesized slop and a few stims. Everything would be alright. Setting up a quick donning of clothing, she set a minor time line in her head, scheduling when would she'd be free to grab a shower. Unfortunately, she got the feeling this Ambassador didn't like being held up. So, smelly or tardy, she imagined he'd expect a marine to be the former. Besides, she has a few moments to catch up with Alenko and that Williams person.

Why was her nose bleeding?

– – – – – – –

Fin Chapter

Okie doke. Summarization - For some reason, Commander Shepard's L2 implants flared up at the wrong time, and caused an enormous biotic surge as the Normandy was passing through a Mass Relay. This damaged the Normandy, and caused Commander Shepard to black out and suffer strange symptoms as her L2 implants refuse to stabilize. Whether or not these images she sees or doing (Beta Chronicle) are real or not is questionable. Or of course, whether or not the original time line (Alpha Chronicle) is real or not due to a side affect of exposure to the Prothean Beacon is also questionable to her. Though both Chronicles seem to have periods of unconsciousness, one's health far worse than the other.

Other than that, I thank you for reading thus far, and would love to hear your comments on this installment of the Sovereign Effect.


End file.
